Mass Effect 2: Doubts and Heartaches
by Meeka Mars
Summary: Uncertain of who or what she is, Shepard searches for Kaidan while trying to hunt down the Collectors. Companion piece to Missing Moments with Aftermath, though can certainly be read separately. In Progress
1. The Lazarus Well

Doubts and Heartaches: The Lazarus Well

"Wake up, Commander."

Someone called to her. A woman. She sounded far away and only vaguely familiar. But Shepard felt sluggish, her body ached. Like the time she was in one of the pressure chambers for increased grav training, her body heavy and hard to move. She tried to open her eyes and light blinded her. She squinted through the burning pain anyway. She could feel again. She couldn't remember when she stopped feeling and it felt good to feel again. She felt… alive.

"Shepard, do you hear me? Get out of that bed now. This facility's under attack."

The woman again. She sounded urgent. Something was wrong. Shepard could feel it in her blood. _A laser canon slicing through the Normandy flashes in her mind. Joker's in the escape pod. She watches helplessly as the intense beam of light cuts through the ship, separating them from each other. Watching the beam ravage the bridge feels like someone's cutting off her arm, yet she can't seem to turn away. She's breathless at the destruction, the power._

_Wires spark and fizzle out. Lights flicker and die. She can see the innards of the ship flying out into space. She's right next to an emergency escape pod release. Her mind jolts as she sees her pilot. She's got to save Joker. She looks across the hall and through the debris at him. Joker's looking at her, frantic. She can see in his eyes everything he can't say. __**Don't… You can make it**__, he pleads with her in those brief seconds. __**Don't do it, Shepard. Don't…**_

_She doesn't have a choice. Shepard feels the electricity of the explosion before it happens, like static building around her. She knows it's coming as her body floats up, knows that she only has one chance to save him. He can't see it through the visor on her helmet. Can't see her eyes telling him, her lips barely mouthing the words…. __**I'm sorry**__. _

_Shepard feels her body lift around, she's already losing control. She pounds the release a mere nanosecond before the explosion knocks her body away. It tosses her like a rag doll, cracking her bones like twigs yet nothing actually hits her. It was like being pushed deep under water by a biotic field, the force and pressure breaking her from the inside out. She feels thrown one direction, then another. Gritting her teeth against the shattering pain, she tries to see if Joker's pod makes it out, but can't keep her eyes on any one thing, lights and darkness flying past her._

"Shepard. Your scars aren't healed, but I need you to get moving. This facility is under attack."

The room was bright around her. Lights flickered behind the glass panes on the other side of the bay and the sounds of gunfire and alarms drowned out her touched her face, feeling the sores on her jaw. She blinked back a halo of light and suddenly she saw it. _A massive ship, more like a space station seemingly carved from an enormous asteroid. It fires again. She watches, powerless, as the Normandy vaporizes in a burst of explosions that blow her away like a child blowing dandelion seeds in the wind. Shepard shuts her eyes floating off in space. Hoping against hope that whatever had just destroyed the Normandy was satisfied and wouldn't go after the crew's escape pods. _

_She gasps at the pain in her chest, her worry for her squad taking over her instincts then realizes her armor is losing pressure when she finally catches the sound of hissing. Shepard arches back to try and find the emergency shut off valve to seal her armor and maybe give her more time. More time to save them… She's gasping for breath, losing oxygen and pressure at a rapid rate. Gripping her throat, she knows she's not going to make it. She gasps deeply, filling her lungs, but can't seem to breathe. She's freezing. It's… excruciating. __**I'm sorry**__, she thinks to her crew. __**I'm sorry for leaving you. I'm sorry for not telling you, Kaidan… **_

_Her body turns and she sees the edge a planet. Suddenly she's on fire. God, it hurts! Shepard opens her mouth to scream but nothing comes out. Tears that should have fallen uncontrollably don't come. She's screaming in silence, tears either frozen or vaporized before they can fall. Her body stiffens under the pressure that keeps building for what feels like hours. And then… it doesn't hurt anymore. There's no more pain, no more need to scream, to cry. She's not cold, not burning… nothing. She stares out in those last brief moments that seem to extend on forever in her mind. The horizon. It's…. beautiful. _

"There's a pistol in a locker on the other side of the room. Hurry!"

Pain radiated through her body, bringing her back to the room, back to the present. She felt odd, like she was moving parts that didn't belong to her as if she were some twisted marionette. Her arms moved when she wanted them to, her legs walked, but it was wrong somehow. Shepard caught herself with a hand on the steel medic bed to keep from falling. She wasn't sure whether she could trust herself to go forward, to walk.

"Grab the pistol and armor from the locker."

The voice drove her. The woman, she blinked, remembering something in a haze. Shepard recalled a man and a woman over her. She was lying down; they were talking… something about her not being ready yet, waking up, sedatives. Wilson… Miranda… doctors? Shepard shook her head. Did she… survive somehow?

"You don't have time to wait around, Shepard. Grab your weapon and armor!"

The woman called more urgently now, more insistent. Shepard clung to it, letting it fuel her muscles to act. She lurched forward to the locker and opened it. Armor, obviously hers, yet not hers. She pulled it out. She'd never worn it that she could remember, but she could tell it was made for her: the N7 insignia, each curve matching her own. Shepard slipped each piece on easily, like a second skin. She immediately grabbed the pistol and tried to reload.

"This pistol doesn't have a thermal clip," Shepard stated out loud before she realized she voiced the thought. She sounded strong despite her throat feeling raw. Good. Gripping the pistol tightly, she felt a little more like herself.

"It's a med bay. We'll get you a clip from… damn it! Those canisters by the door are going to blow! Get behind cover, now!"

Shepard's instincts forced her to duck down behind the counters. The room seemed to vibrate in anticipation and she felt her heart skip a beat. She breathed in deeply through her nose, settling her nerves until her heart pumped steady and strong. Releasing her fear, she focused on the moment. Point A to point B, she told herself.

"Keep your head down, Shepard! Shield yourself from the blast!"

The door burst open in a heated blast and adrenaline pulsed through her veins. Shepard stumbled forward at first, her eyes still blurry, halos of light shimmering in her peripheral vision. Everything was hard and bright. Her legs felt strange, like when she first steps off a treadmill onto real ground. Nothing felt real, tangible, except the pistol in her hand. She gripped it tightly, using it as a lifeline to this hell. A lifeline to survival.

"Someone's hacking security trying to kill you. Look for a thermal clip for your pistol!"

Shepard scanned around the ground and crates and spotted a body on the floor. Unsurprisingly, she didn't recognize him or anything else in this place. It was a waking nightmare, but one she was sure had to be real. The pain coursing through her body, the aches, they told her she was real. They told her she was alive, awake. She grimly snatched a couple extra thermal clips from the dead man's belt and loaded her weapon, keeping a keen eye ahead for approaching targets.

"Looks like they set up a barricade to try holding the mechs off."

She heard a mech as it patrolled the other room and Shepard ducked down low behind a small barricade. Her blood raced. She breathed in. Suddenly everything was clear. Her ears caught the clank clank of mech steps behind the blaring of an alarm, the echoes bouncing in the room giving her its general position.

"Look out!"

The woman's voice faded into the background. Shepard felt her training kick in. She wanted this, needed this. Immediately she leapt over the barricade and rolled to the next cover. Her back strong, her legs balanced. Shepard clenched the pistol, feeling the tight resistance of the trigger with her finger, the thickness of the handle solid in her hands. She gracefully shifted out of cover and took the mech out quickly, efficiently. Pop, pop!

Its red face fizzled then blanked out and Shepard drew in a steady breath. This was what she was made for. She was going to find out what the hell was going on here and rescue her crew. Shepard clenched her fist. It still felt alien, like a new soldier under someone else's command. But it worked. And somewhere deep in her mind, she knew time would restore whatever it was she had lost. But right now, she had a mission. Shepard popped the heat sink and reloaded her gun. This was her dance.


	2. From the Ashes

Doubts and Heartaches: From the Ashes

Despite the Illusive Man's intent suggestion that she hit Omega right away and find Dr. Solus, Shepard chose to visit the Normandy's crash site first. She couldn't move forward if she was stuck in the past. It surprised her, how chill and barren the planet was and how undisturbed the wreckage for the Normandy had been. Didn't they send a search party? Wouldn't the Alliance have scoured the wreck for survivors? And if so, wouldn't they have already collected their soldiers' lost dog tags? Two years the Normandy lay untouched, written off… forgotten. Had she been forgotten too?

Shepard placed her broken N7 helmet down and sat in the chair at the desk. Sighing, she emptied the dog tags onto the desktop. She pulled one out of the pile and read the name, Raymond Tanaka . His face flashed in her mind, a tall dark haired man that worked in engineering with Adams. She shook her head sadly, while pulling out another, Caroline Grenado. Young and fresh out of the academy, she worked in decryption up on the bridge. The next tag belonged to Carlton Tucks, a quiet soldier who worked on the Mako's maintenance. Did their families know they were gone? Were all these soldiers just missing in action or were they declared dead after the survivors were rescued, like she had been?

She read through the tags. Abishek Pakti, Silas Crosby, Talitha Draven, and her sister Rosamund Draven. Their dog tags weighed heavily in her hand, their faces just flashes of distant memories. People she barely knew, soldiers who depending on her to lead them. Some of these men and women risked being court-martialed when she commandeered the Normandy. Orden Laflamme, Mandira Rahmann, Alexei Dubyansky, Harvey Gladstone, Hector Emerson, Addison Chase, Jamin Bakari, Helen Lowe, Germeen Barrett, Amina Waaberi. These were the servicemen she couldn't save.

Slowly she rubbed the raised lettering on the tags, each letter pounded out by a massive machine, each soldier forged in countless hours of grueling training. Robert Felawa, Shepard remembered him and his partner, Monica Negulesco. The investigators assigned to assess the crew's loyalty and capability status, mostly just a formality to satisfy parliament. Shepard remembered planning with Kaidan in the mess one afternoon, what they would do once the AIA Agents had left. Now those internal affairs agents were dead. Marcus Greico, the Normandy's cook, she recalled he'd made ration pancakes the morning of the attack. Charles Pressly, her old XO. Pressly had insisted she take a longer break to sneak in some time with Kaidan, not even an hour before the Normandy was destoryed. She clenched the tags in her hand.

The tears wouldn't come and she punished herself in her mind for that. How could she not cry for the soldiers lost while on her watch? They were her men! Her women! She was supposed to protect them! She was their Commander! Shepard threw her helmet at the wall, it hit and rolled back toward her, reaching her feet. The visor looked up at her and she collapsed forward, burying her head in her hands. Still no tears. She cursed at herself for that. She looked down in through the broken visor and slowly picked up the helmet, staring at it. Of everyone that had died, she survived.

Two years. The thought haunted her. How could she have been gone for two years? _Nothing but meat and tubes_… Jacob Taylor's voice echoed in her mind. Shepard tried to wrap her mind around it. She clenched her fist, feeling that strange awkwardness. When she had woken up, she couldn't quite place why. Now she knew. Flexing her arm, she could almost feel each cybernetic bone. Her entire right arm… not hers. Her left leg, not hers. Half of her ribs, parts of her back, her entire left hand up to at least her elbow, all not her anymore. In fact, most of her felt… Shepard shook her head. What was she then, if she wasn't her anymore?

Joker seemed to think she was fine. Treated her even better than when they served on the SR1. Shepard was sure that was simply because he was so glad to have her back, or maybe he was just happy to be flying again. Then Tali had said it was definitely her. Shepard recalled that feeling of relief when her quarian friend had announced that much. She felt a tiny bit of that doubt etch away as Tali trusted her, talked to her, worked with her. Shepard wished she could have talked to more of them. Garrus, Wrex, Liara…. Kaidan. She sighed, looking at her helmet. Shepard clutched it tighter in her hands and stared at cracks in the visor, her reflection broken, just like she was. _Who am I now?_

_The Illusive Man wanted you exactly as you were_, Miranda's frank admission echoed in her mind. What better way for Cerberus to control her than to make her believe they didn't control her. What if Cerberus really had implanted her with some sort of control device? Shepard didn't feel controlled in anyway. In fact, she felt just the opposite. She felt more lost than ever. Without the Alliance, without the people she had come to trust and care for, who was she? What was she if she wasn't an Alliance soldier? Was she a terrorist now? A rogue Spectre like Saren just _thinking_ she was doing the right thing? Wasn't Saren only doing what he thought would save organics from the reapers? Was she any better at this point? She had to believe she was or she might just go crazy.

Doubt itched at her though. She hated feeling like this: the not knowing. Then there was the Illusive Man himself. If he had implanted her with some sort of control device, why was he working so hard to convince her to help him? He appealed to her inherent nature to serve and protect. Help humanity, he touted. It was an obvious ploy to get her to cooperate, yet it worked. She couldn't turn her back on these people, on her people. Cerberus was wrong to do a lot of other things, but this… Shepard had to believe that what she was doing was right. And the Illusive Man seemed to know just what to say to get her to help. He wouldn't go through all that trouble if he could force her to do what he wanted with a flip of a switch, right?

She gently put the helmet back on her desk. It watched over the dog tags scattered there. She noted sadly that it had been her job to watch over them once, and she failed.

"How do you deal with losing soldiers under your command?" Kaidan's words after Ash's death echoed back to her. He'd never lost anyone. Not until Jenkins at least. And then on the Normandy he'd not only lost Jenkins, but Ash as well. When Shepard thought about it, technically, he'd lost her too. Was that her fault? Did death just follow her wherever she went?

"I promise to do better by them next time," Shepard told him. It was the truth and it was a lie. The truth was that she did promise them that. She promised it to herself, every time. The lie was that she dealt with it. Mostly she had to harden herself, not get close to her soldiers. And she had done a damn good job of it until serving on the Normandy. She wanted to tell Kaidan that now, wanted to be wrapped in his arms and confess all the things she couldn't do, all the things she wasn't strong enough to see through. I _couldn't save them_, she whispered. _I can't even cry for them_.

It felt like they'd only had that conversation a few months ago. The pain from Ash's death was still slightly fresh, made even more so by visiting the remains of the Normandy. She couldn't believe she'd been in a coma for two whole years. Wasn't she just talking with Kaidan about how they couldn't break regs with the AIA on board a few weeks ago? Wasn't Garrus teasing Tali about her avoiding her pilgrimage to get in a few more shots at the geth a week before? Joker giving Pressly a hard time, Wrex teaching Garrus more tactics…How could it have been two years ago? Did any of her crew know she was alive? Did they care?

To Tali, Shepard's sudden appearance was a surprise. Maybe none of them knew she was alive. If they did, would they come back? She had been so sure they would when she woke up but after the Illusive Man told her how they had all moved on, she had doubted it a little. Then when Tali told her she couldn't… Shepard's heart dropped. They wereher crew. But she'd been gone. She'd abandoned them. For two entire years, it seemed. How could she even ask them back after leaving them for so long_? It's not your fault_, she told herself. But then, whose fault was it? Should she have woken up? Why didn't she wake up sooner?

_I thought you were still a work in progress. _Jacob's comment made her wonder. She wasn't just in a coma and her injuries were extensive, but would that really take two years for her to heal? Shepard shook her head. What injury would take two years to heal? Plus all of the strange pieces of data recordings she found while floundering on that space station. Billions of credits sunk into Project Lazarus, just to bring her back? Back out of a coma? Back from the dead? She scoffed at that. No doctor, no matter how good, could bring someone back from the dead, right? Dead was dead, end of story.

She glanced at the dog tags. Why her? So she was the Commander of the Normandy. She led the team that took down Saren, helped take down Sovereign. It's not like she did it by herself. There was an entire crew, an entire ship backing her. What made her more special than any other Commander out there? Didn't she just happen to be in the right place at the right time? So much of what they accomplished hinged simply on blind luck. Did they bring her back just because she's lucky? Or was she lucky because they brought her back?

Shepard couldn't think anymore about it. She carefully put the dog tags in a case, reading each name, remembering what she could of the soldiers one last time. No tears, just silence. It seemed fitting though, the quiet; nothing but the soft hum of the new Normandy lulling her into her own memories. Her conversation with Kaidan echoed in the back of her mind again. _I'll do better by them next time…_

Whether she was herself or not, Shepard was here now. She had a second chance for whatever reasons, better or worse. And people needed her now. She wasn't going to turn her back on them. With this new crew, she might not trust them all but they were her crew none-the-less. She was their Commander and right now was her 'next time'. Shepard vowed that no matter what, she was going to do better for it. For them.


	3. Preoccupied

Doubts and Heartaches: Preoccupied

They had been working on Omega for the past couple days. Already Mordin Solus had been recruited and a Collector plague averted. Mordin seemed more than capable of handling himself and had even debugged the lab of all the Cerberus surveillance. Shepard made a mental note to have Mordin clear out some other parts of the ship as well, like her cabin. She didn't need Cerberus spying on her any more than they already were. After all, having two Cerberus agents and a Cerberus AI on the ship was probably all the surveillance the Illusive Man needed. No sense in giving him video and audio with those reports.

Aria T'Lok had been her main source of information on Omega since Shepard arrived. Strangely enough the asari was more than willing to dole out information on Mordin and Archangel despite her saying that information wasn't free. Of course being a previously dead Spectre probably helped. That and Shepard was fairly certain Aria wouldn't miss Archangel or Dr. Solus if she vacated them from Omega. It seemed Aria rather preferred the thugs and gang members to capable doctors and vigilantes. After all, she'd just updated Shepard on how to get to Archangel.

"You look a little strung out. You should find a nice young man to keep you warm at night," Aria crooned as Shepard stood up. She shook her head as she left. She did have a nice young man, she just didn't have any idea where he was or what he was doing at the moment. That and Shepard wasn't entirely sure if Kaidan still cared about her. After all, it had been two years. She was still having trouble wrapping her head around that. Two years. So much could happen in that amount of time.

"She's right you know," Miranda commented once they reached the bottom of the stairs.

"What?"

"I know about you and Lieutenant Alenko, Shepard. You've been trying to access his files on the Normandy, but you won't find anything. Everything on Alenko in the last fifteen months has been extremely classified," Miranda stated. "He's moved on, Commander. You should too."

"I should have known you'd have my personal logs tapped. You read all my messages too?" Shepard quipped.

"Just the ones that look important," Miranda answered casually. "The Normandy is a Cerberus ship, Commander. You'd do well to remember that."

Shepard stopped and turned to face the Illusive Man's agent. She stared her down, "So long as you remember that I'm not working for Cerberus and my personal affairs are none of your business."

"The Illusive Man wants you committed, Shepard. You can't be focused on stopping the Collectors if you're spending all your free time trying to find out what happened with your old fling."

"Kaidan was not a fling," Shepard interjected. "And if you keep talking about things that aren't any of your concern, you'll find out just how effective I can be with a preoccupied mind."

"Oh?" Miranda piqued. "You could have fooled me. And everyone else at the Alliance. There was no real relationship there. Even after the final reports were filed, the Alliance brass didn't even try to pursue your little regulation breach despite a well documented anonymous tip."

"You don't expect me to believe that Cerberus had surveillance on the SR1," Shepard started.

"Of course not. The tip didn't come from Cerberus at any rate, just crew member who thought it best to include all of the Normandy's interactions. Luckily for him, he was very good at guarding his anonymity." Miranda paused to let that sink in. Whether or not this crew member was working for Cerberus now would be pointless to ask since Shepard knew Miranda would never tell her.

She wondered though, how deeply imbedded Cerberus was if they could get their hands on reports like that. She knew Cerberus had been a black ops division working with the Alliance and that they had gone rogue when she was investigating Saren, maybe even before that. But she never did find out how deeply entrenched they were into the system. As far as she knew, the Illusive Man might have information even Anderson was unaware of, though if that had been the case, he would probably have more on Kaidan's whereabouts at the very least. The fact that both him and Miranda haven't been able to access the Lieutenant's files made Shepard wonder if that was due to Kaidan working on very classified missions, which he most definitely had the skill set for, or whether they were just trying to keep her in the dark, which was also very likely.

Shepard hoped for the former. At least it put Kaidan a little further out of Cerberus' reach and hopefully out of any danger associated with them. So far Shepard wasn't entirely convinced of the Illusive Man's story and his goal of wanting to help humanity. Maybe he did, but his methods were nothing short of monstrous. Did that make her a monster then? Shepard didn't like the thought. How could she be certain she was who she thought she was and not some Cerberus puppet? She watched Miranda warily. If she had been a puppet, the Illusive Man probably wouldn't have one of his top lackeys watching her every move. In that case, Miranda's spying was actually a comfort rather than a threat.

"I don't care what reports you have on Lieutenant Alenko and I, the point is it's none of your business."

Miranda observed her for a moment then finally replied. "Alright. But that still doesn't change the fact that you should move on."

"I'll move on when I'm good and ready." Shepard wasn't up for discussing this anymore. She knew she wouldn't find any information on Kaidan through the normal routes, and with confirmation that Miranda was watching her every move and no doubt reporting it all to the Illusive Man, she would have to resort to other methods to track him down, if only to protect him should she come across something she could actually use. A visit to Anderson at the Citadel would be a good start and leaving the Cerberus squad behind would help even more.

"Hopefully it's sooner rather than later," Miranda added.

Shepard smirked. Cerberus wasn't going to get the best of her, "Don't count on it."

* * *

_Author's Notes: My hubby started up an ME2 game a few days ago, so I've have ME2 on the brain lately. Between writing for Missing Moments I've been writing out some of the things I thought while playing ME2 forever ago._ _This story actually goes along with Missing Moments, but can certainly be read apart from it. I just wanted to write out some of Shepard's struggles. Also writing Kaidan's in another fic, Aftermath. Basically Prequels that help expand upon some of the things happening and coming up later in Missing Moments._


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